ETV3L

protein-coding

ETS variant transcription factor 3 like, the group of ETS transcription factor family

Gene summary

Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific. Predicted to be involved in cell differentiation and regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001004341.2

Inheritance

—

ClinVar variants

U:65B:19

Top phenotype

ETV3L-related disorder

gnomAD constraint

pLI —, LoF o/e 0.88

Max pathogenic AF

—

Genomic locus

chr1:157,092,043-157,112,412

External References & Databases

Ensembl (ENSG00000253831)

Transcript & Mutation Effects

hg38 • Region Span ~20.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ETV3L variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 72

not providedTotal: 6

ETV3L-related disorderTotal: 6

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001004341.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				2 clinvar	2 clinvar	4
missense			64 clinvar	12 clinvar	2 clinvar	78
nonsense				1 clinvar		1
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)						0
Total	0	0	65	15	4	84

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 14 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001004341.2	RefSeq	NP_001004341.1	5	MANE Select
ENST00000454449.3	Ensembl	ENSP00000430271.1	5	MANE Select
ENST00000671886.1	Ensembl	ENSP00000500322.1	5	Standard
ENST00000671886.2	Ensembl	ENSP00000500322.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

negative regulation of transcription by RNA polymerase II
regulation of transcription by RNA polymerase II
cell differentiation

Molecular Function

DNA-binding transcription factor activity, RNA polymerase II-specific
DNA-binding transcription repressor activity, RNA polymerase II-specific
sequence-specific DNA binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000454449
Coding exons: 5
Length: 7765
Individuals with no LoFs: 125640
Homozygous LoFs: 0
Heterozygous LoFs: 106
Defined: 125746
p: 0.000422

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.348	217	203	1.07	0.0000114	2306
Missense (PolyPhen)		53	53.319	0.99402		635
Synonymous	-0.142	89	87.3	1.02	0.00000515	751
Loss of Function	0.427	12	13.7	0.875	8.56e-7	131

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0012	0.0012	notable
Latino/Admixed American	0.0021	0.0017	notable
Ashkenazi Jewish	0.00042	0.00040	rare
East Asian	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00016	0.00016	rare
South Asian	0.000065	0.000065	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Transcriptional regulator. {ECO:0000250}.;

Intolerance Scores

LoFtool: 0.772
RVIS EVS: 1.44
RVIS percentile EVS: 95.08

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium